Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 1LAN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PRO 4.4 1.0 + - - -
245A LEU* 4.0 26.7 - - + -
246A VAL 3.1 24.8 + - - +
247A PHE* 5.3 0.7 - - + -
351A PRO* 3.5 3.5 - - - +
352A LYS* 1.3 89.3 - - + +
354A ILE* 1.3 68.5 + - - +
355A ILE* 4.2 22.7 - - + -
381A TRP* 4.1 28.9 - - + -
382A LEU* 4.6 8.3 - - + -
442A HIS* 3.8 2.0 - - - -
444A LYS* 3.4 18.4 - - + +
478A PHE* 4.7 2.9 - - + -
482A PHE* 4.7 8.1 - - + -
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL* 3.5 9.2 - - + +
248A VAL* 4.5 6.7 - - + -
343A LEU* 4.0 25.8 - - + -
346A ALA* 4.2 20.2 - - + -
347A HIS* 4.1 23.6 - - + +
351A PRO* 3.6 24.7 - - + -
353A VAL* 1.3 80.1 - - - +
355A ILE* 1.3 64.7 + - - +
382A LEU* 4.6 0.2 - - - +
440A VAL* 5.4 1.8 - - + -
442A HIS* 3.9 26.0 - - + -
444A LYS 2.9 9.7 + - - +
445A TRP* 3.2 14.1 - - + -
446A ALA 2.9 24.9 + - - -
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL 2.9 10.2 + - - +
247A PHE* 3.1 32.7 - - + +
248A VAL* 2.8 22.5 + - - +
280A ILE* 4.8 2.5 - - + +
353A VAL* 4.2 12.3 - - + -
354A ILE* 1.3 81.0 - - - +
356A ASN* 1.3 69.3 + - - +
382A LEU* 4.4 11.2 - - + -
386A LEU* 4.5 10.5 - - + -
446A ALA* 3.5 14.8 - - + +
448A LEU* 4.3 15.7 - - + -
475A LEU* 4.6 10.5 - - + -
478A PHE* 3.6 37.2 - - + -
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Residues in contact with ASN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 3.0 28.7 - - + +
280A ILE* 5.1 0.4 - - - -
339A LEU* 4.1 18.2 - - + +
343A LEU* 4.1 13.7 - - + +
354A ILE 4.3 0.4 - - - -
355A ILE* 1.3 76.6 - - - +
357A ALA* 1.3 66.1 + - - +
436A LEU* 4.2 3.6 - - - +
445A TRP* 2.9 30.2 + - - +
446A ALA 3.0 7.8 + - - +
447A HIS* 3.0 37.2 + - - +
448A LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL 2.9 5.3 + - - -
249A GLY* 3.5 1.6 - - - -
250A LYS 3.3 19.9 + - - -
276A GLY* 3.4 8.5 - - - +
279A THR* 4.0 14.8 - - - +
280A ILE* 3.7 24.0 - - + -
339A LEU* 4.9 0.5 - - - +
355A ILE* 5.9 0.2 - - + -
356A ASN* 1.3 78.0 + - - +
358A ALA* 1.3 63.5 + - - +
448A LEU* 3.3 20.6 - - + +
450A ILE* 4.8 6.7 - - + -
471A PRO* 5.9 0.9 - - + -
475A LEU* 5.4 1.8 - - + -
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LYS* 3.6 24.2 - - + -
276A GLY* 4.1 7.1 - - - -
339A LEU* 3.9 19.5 - - + -
357A ALA* 1.3 78.1 - - - +
359A THR* 1.3 55.2 + - - +
360A LEU* 2.9 18.9 + - + -
447A HIS* 4.5 4.9 - - + -
448A LEU 2.9 7.9 + - - +
449A ASP* 3.3 5.4 - - - +
450A ILE* 2.8 32.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il